Team:Sydney Australia/Patent Law

Aim


In constructing the sequence of a single chain insulin we had to ensure that our sequence was not under any existing patents so that we could submit our sequence into the Open Source iGEM registry. With a bit of help from Maxwell Lawyers we went through several single chain insulin patents, method patents and existing patents for current insulin dispensing devices/therapeutics using the FDA orange book. The goal was to make sure our work did not come under any existing patents so we would not infringe any ownership rights.

Importantly, we recognise the difficulty of being thorough with all existing patents and the content provided is not intended to be legal advice and should not be used as such. To determine whether you are infringing a patent; the best course of action is to seek a qualified patent lawyer.

To examine the way we approached patents - please click on the links below for easy navigation to each section.

How to read a patent


After our chat with Uppsala (check it out in collaborations), our team realised that patents are a very poorly understood area, particularly for young aspiring scientists with new and challenging ideas.

With a resident legal student in our team - we created a quick checklist on How to read a patent

KEY CONSIDERATIONS

1. Patents give an exclusive commercial right to the invention aka. a monopoly

2. The "claims" of a patent, detail what is covered by the patent.

3. If it is NOT in the patent; it is NOT patentable.

And it is with this checklist that we approached the analysis of a wide range of patents below.

1. Single Chain Insulin Patents


Although our team attempted to be thorough, we recognise that not all patents can be checked. However, we targeted patents with the greatest relevance to avoid legal suits that may arise. Our primary concern was single chain insulin patents since they have only been recently explored in greater depth and quoted to have benefits like enhanced thermostability. As these single chain insulins are likely to be the next insulin product in the market, we wanted to create one, outside the scope of existing patents, to characterise and compare our product.

Importantly there is an exception in patents for research purposes. This means that if the work you performed is for research purposes only, you do not infringe the relevant patent. You cannot however, submit the part into the open source registry or try and commercialise it. As we are submitting 'Winsulin,' our single chain insulin, it must not be patented.



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DIMARCHI ET AL.

Single Chain Insulin with high bioactivity

Patent No: US 9458,220 B2

October 4th 2016

 

 

CLAIM

 

COMPARISON WITH OUR SEQUENCE

 

Y/N

 

A single chain insulin agonist analogue with stricture of B-LM-A wherein B represents an insulin B chain comprising the sequence R22X25LCGX29  and A represents an insulin A chain comprising the sequence

GIVX4X5CCX8-R13

 

Both insulin A and B chains involve R groups which stand for modifications eg. carboxylation. As our insulin B chain does not contain any modifications (except for a substituted glycine on the A chain), our construct is outside the patent

 

N

 

 

Furthermore the linking moiety linking the carboxy terminus of the B chain to the amino terminus of the A chain; further wherein the linking moiety is an 8 amino acid sequence comprising of the sequence X51X52GSSSX57X58 wherein

X51 = group consisting of glycine, alanine, valine, leucine, isoleucine, isoleucine and ornithine

X52 = any amino acid other than tyrosine

X57 and X58 are independently selected form the ground consisting of arginine, lysine and ornithine

 

 

Our amino acid sequence is squarely outside the scope of 8 amino acids.

 

Even if we did fall within the claim; we do not contain the 8 amino acid sequence using both potential orientations

 

X51 is glutamine or arginine in our sequence

 

 

B-chain QR . . . KR A-chain

N

 

The LM also requires the sequence of GAGSSSRR or a sequence that differs from GAGSSRR by 1 or 2 amino acids

 

Our sequence is 12 amino acids long and differs by more than 4 amino acids.

N

 

LM represents linking moiety linking the carboxyl terminus of the B chain to the amino terminus of the a chain, wherein said linking moiety is an 8 amino acid sequence consisting of X51X52X53X54... wherein X51 is selected from the group consisting of glycine, alanine, valine, leucine, isoleucine and proline

 

Similarly, the patent claim is over an 8 amino acid sequence. Applying the same principle our;

 

X51 is glutamine or arginine (depending on orientation) and outside the scope

N

 

LEE ET AL.

Single Chain Insulin Analog and a polynucleotide sequence encoding the analog

Patent No: US 6,630,348 B1

October 7th 2003

 

 

CLAIM

 

COMPARISON WITH OUR SEQUENCE

 

Y/N

 

A single chain insulin analogue compound of formula (I) having the properties of greater insulin receptor binding activity than proinsulin and less insulin receptor binding activity than insulin:


B chain -  X
A chain wherein:

 

General B X A chain single chain formula

Y

 

B and A chain are human insulin chains, respectively and,

 

 

Our B and A chain are human insulin chains although our A chain includes a modification (A21 substitution into glycine)

 

N

X is a joining peptide of about 5 to 18 amino acids comprising the following sequence: Gly-Gly-Gly-Pro-Gly- Lys-Arg

 

Where the term comprisingis included, the patent requires that the specific sequence named MUST be part of the linker region.

 

Although our sequence is 12 amino acids long, it does not contain the GGGPGLR identified in the patent

 

N

 

LEE ET AL.

Single Chain Insulin Analogs

Patent No: EP 1 193 272 B1

October 30th 2004

 

 

CLAIM

 

COMPARISON WITH OUR SEQUENCE

 

Y/N

 

A single chain insulin analogue compound of formula (I) having the properties of greater insulin receptor binding activity than prosinsulin and less insulin receptor binding activity than insulin:

 

B Chain UI Zn Y ZI Un A chain

 

 

 

B and A chain are human insulin chains respectively and

 

 

We have a modified A chain

N

 

U is an arginine or lysine residue

 

Our U is glutamine

N

 

Z is a glycine

 

 

Z Is Glycine

Y

 

 

I is an integer of 2 – n

N is an integer of 0 or 2 and

 

The maximum size of the linker sequence when considering this is 9 amino acids. Since our sequence is 12 amino acids they are outside the scope

 

N

 

Y is glycine-proline-glycine, or alanine-proline-glycine-aspartic acid–valine, or tyrosine-proline-glycine-aspartic acid-valine, or histidine-proline-glycine-aspartic acid-valine.

 

 

 

Our sequence has no proline

 

N

 

KJELDSEN ET AL.

Single Chain insulin

Patent No: EP 1692168 B1

December 3rd, 2004

 

 

CLAIM

 

COMPARISON WITH OUR SEQUENCE

 

Y/N


Single-chain insulin for treatment of type 1 diabetes and type 2 diabetes having the formula

B(1-26)- X1 - X2 - X3- X4- A (1-21),



B - linker - A formula

Y


B(1-26) is a peptide chain consisting of the first 26 amino acid residues of the B chain of human insulin counted from the N-terminal end of the B chain or an analogue of the B-chain with one addition or one deletion of one of the amino acid residues in the B-chain or derivative of the B-chain being chemically modified by introducing a group in the side chain in one or more positions of the B-chain or by oxidation or reduction of the side chains of the amino acids residues in the B-chain,


Our B chain consists of 28 AA. Although the patents contain different versions eg
an analogue of the B-chain with one addition or deletion the total length of the B-chain must STILL be 26AA.

N


and A(1-21) is the natural insulin A chain or an analogue thereof with one addition or one deletion of one of the amino acid residues in the A-chain or derivative of the A-chain being chemically modified by introducing a group in the side chain in one or more positions of the A-chain or by oxidation or reduction of the side chains of the amino acids residues in the A-chain, wherein

In our sequence construct the A chain is 21 amino acid however it is a modification of the natural protein. It does not fall within an 'analogue' as there is no complete addition/deletion of an amino acid.

N


X4 does not contain two adjacent basic amino acid residues and wherein the single-chain insulin has an affinity to the human insulin receptor of at least about 20% of that of human insulin if the single-chain insulin molecule is not chemically modified by acylation.

We have 2 adjacent basic amino acid residues and the affinity cannot be tested

N


wherein X1 is Thr, Lys or Arg


X1 is glutamine

N


X2 is Pro, Lys or Asp,


X2 is arginine

N


X3 is Lys, Pro or Glu,

 

 

X3 is glycine

N

 

X4 is a peptide sequence with the following formula Xa-Xb-Xc-Xd-Xe-XfXg (SEQ ID NO:129) wherein

 

Xa is selected from the group consisting of L, R, T, A, H, Q, G, S and V;

 

Xb is selected from the group consisting of W, G, S, A, H, R, and T;

 

Xc is selected from the group consisting of L, Y, M, H, R, T, Q, K, V, S, A, G and P;

 

Xd is selected from the group consisting of R, A, Y, M, S, N, H, and G;

Xe is selected from the group consisting of S, R, A, T, K, P, N, M, H, Q, V, and G;

 

Xf is selected from the group consisting of G and A; and

 

Xg is selected from the group consisting of K, R, P, H, F, T, I, Q, W, and A,

The total linker length that can be formulated from Xa Xg is 7 amino acids with the three other residues for X1 – X3. This totals to a maximum linker length of 10 amino acids. Our linker is 12 amino acids long.

N

 

WEISS ET AL.

Fibrillation-resistant insulin and insulin analogues

Patent No:EP 2074140 B1

April 6th, 2009

 

 

CLAIM

 

COMPARISON WITH OUR SEQUENCE

 

Y/N


An insulin analogue comprising a single chain polypeptide containing an insulin A-chain polypeptide and an insulin B-chain polypeptide connected by a truncated linker,

 

Our linker is truncated from the entire C-peptide to 12 amino acids and has the general formula of B-X-A where our linker is

QRGGGSGGGQKR

 

Y

 

wherein the truncated linker is a polypeptide selected from the group consisting of:

 

 

a polypeptide having the sequence GGGPRR

 


No proline

N

 

a polypeptide having the sequence GGPRR

 


No proline

N

 

a polypeptide having the sequence GSEQRR

 


No glutamate

N

 

a polypeptide having the sequence RREQR

 


No glutamate

N

 

a polypeptide having the sequence RREALQKR

 


No glutamate

N

 

a polypeptide having the sequence GAGPRR

 


No proline

N

 

a polypeptide having the sequence GPRR

 


No proline

N

 

wherein the insulin B-chain polypeptide optionally contains one or more of:

an aspartate substitution at the position corresponding to position B10 of insulin,

a lysine or an aspartate substitution at the position corresponding to position B28 of insulin, and

a proline substitution at the position corresponding to position B29 of insulin

 

Our B-chain is native human insulin

N


and wherein the insulin A-chain polypeptide contains a histidine substitution at the position corresponding to position A8 of insulin.

Our A-chain does not contain the relevant substitution

N

 

STOWELL ET AL.

Chemically and thermodynamically stable insulin analogues and improved

methods for their production

Patent No: US 9006176 B2

October 16th 2012

 

 

CLAIM

 

COMPARISON WITH OUR SEQUENCE

 

Y/N

 

A single chain insulin (SCI) compound of formula a(I):

 

B chain - C – A Chain (Formula (I))

 

having the properties of higher affinity for the insulin receptor and lower affinity for the IGF-1 receptor as compared to those of native proinsulin with chemical and thermodynamic degradation profiles such that the SCI can be formulated and stored for extended periods of time without refrigeration;

 

 

Correct linker formulation of B-linker-A

Y

 

W herein B chain and A chain are modified human insulin chains; and

 

 

Only the A chain is modified 

N

 

Wherein C covalently links the C-terminus of the B chain to the N-terminus of the A chain, and is a peptide of 5 amino acids comprising the following sequence: Y-P-G-D-X (SEQ ID NO: 1); wherein X is any amino acid;

 

No proline (P) and no aspartic acid (D)

N

 

wherein the B chain is modified from a native human insulin B chain (SEQ ID NO:11), and A chain is modified from a native human insulin A chain (SEQ ID NO:10), wherein the modifications comprise one or more mutations at

 

(1) Gln5, Gln15, Asn18, or Asn21 of SEQ ID NO:10, or

 

(2) Asn3 or Gln5 of SEQ ID NO:11; resulting in enhanced resistance to deamidation.

 

 

 

 

 

B is not modified and A chain does not have similar modifications, rather an addition at residue 1 without the purpose of resisting deamination.

N

2. Method Patents


In looking at patents, we first considered looking at different methods of production – particularly whether or not Bacillus secretory methods are patented for insulin production.

From a preliminary search, Bacillus secretion has been previously patented however most are now expired. If it is possible to find a patent using the same method of production as a previously patented product, it will not infringe anyone elses intellectual property.

relatively important PATENT STUFF

 

STAHL ET AL.

Method for Producing Heterologous Proteins

Patent No: US4801536A

November 10th, 1985

STAHL ET AL.

 

CLAIMS

 

COMPARISON WITH OUR METHOD

Y/N

 

Status: EXPIRED. Now this patent has expired. Importantly it covers our
project as we have a heterologous protein being attached via a secretion tag to the actual plasmid vector design.

 

Y

 

A method for producing a heterologous protein in a bacterial host cell such that the protein is exported from the host cell into the culture medium, the method comprising culturing in a bacterial culture medium a genetically engineered bacterial strain containing a fusion DNA sequence which comprises a first nucleotide sequence encoding at least an N-terminal portion of a flagellin protein native to the bacterial host cell species and a second nucleotide sequence encoding the heterologous protein, said first nucleotide sequence being linked via its 3' terminus to the 5' terminus of the second DNA sequence and said fusion DNA sequence being operatively linked to an expression control sequence and wherein said N-terminal portion results in the export of said heterologous protein.

 

 

 

 

Our plasmid falls directly into this means of production. As this patent has since expired and we fall under it – the methods that are encoded are free to be used and thus not for law suit.

Y

 

A plasmid as identified in any of Tables 2 to 5 of the specification by the designation pSPA or pSPB.

 

WB800 plasmid

N

 

A DNA sequence flanked by and in proper reading frame with a non-wild type open reading frame encoding a secretory signal sequence having the amino acid sequence: pSPB4, pSPB9, pSPB19, pSPB20, pSPB23, pSPB28

 

 

None of the plasmids mentioned are being used nor are the AA sequences that are described in greater detail in the patent

N

 

KOVACEVIC ET AL.

Method for expression and secretion in Bacillus

Patent No: US5032510A

July 16th, 1991

 

 

CLAIMS

 

COMPARISON WITH OUR METHOD

Y/N

 

STATUS: Expired. The invention method claimed is now open source.

 

Y

 

1. A method for expressing a peptide in Bacillus, said method comprising 

 

We are expressing a peptide/polypeptide in Bacillus

 

Y

 

a) transforming a Bacillus host cell which is rendered competent for transformation with a recombinant DNA expression vector which is selectable and capable of replication in said host cell, said vector comprising 

Our Bacillus host cell was made competent specifically for recombinant DNA uptake. The expression vector is also capable of replication

Y

 

1) the transcriptional and translational activating sequence of the Staphylococcus aureus nuclease gene and

2) a cloned DNA sequence that codes for a polypeptide, and

 

This vector however does not include a Staph. Aureus nuclease gene.

Winsulin is a single poly-peptide chain, while Insulin is a dual-peptide complex

N

 

b) culturing said transformed cell under conditions suitable for expression of said polypeptide, subject to the limitation 1) that said cloned DNA sequence that codes for said polypeptide and said transcriptional and translational activating sequence are immediately adjacent, in translational reading frame and positioned for expression of said polypeptide and 2) that said cloned DNA sequence that codes for said polypeptide is exclusive of the nucleotide triplet that codes for the N-terminal amino acid of said polypeptide when said amino acid is methionine.

 

This potentially could be an issue, depending on the reading and interpretation. However, since we fall outside of the above key aspects of this individual claim, we are still in the clear.

 

N

 

BERKA ET AL.

Heterologous polypeptide expressed in filamentous fungi, processes for their preparation, and vectors for their preparation

Patent No: EP0369817B1

April 24th, 1996

 

 

CLAIMS

 

 

COMPARISON WITH OUR METHOD

 

Y/N

 

Status: EXPIRED

The expiry date of this patent is extremely critical as it patents the production of proteins in a Bacillus cell with multiple gene knockouts. Importantly, the strain used by us, WB800 contains 8 protease knockouts and thus falls within the scope of this patent. As the patent has expired –this means of production is available for use.

 

Y

 

Claim 1

A Bacillus cell characterised in containing a mutation in the epr gene, said epr gene encoding a protein comprising the amino acid sequence of Figure 6 or an evolutionary homologue thereof of other Bacillus species, having protease activity, said mutation resulting in inhibition of the production by said cell of proteolytically active epr gene product.

 

We have a mutation in the epr gene in WB800, which renders the EPR protein inactive such that it does not have a proteolytically active epr gene product

Y

Claim 16

A method for producing a heterologous polypeptide in a Bacillus cell, characterised in comprising: introducing into said cell a gene encoding said heterologous polypeptide, modified to be expressed in said cell, said Bacillus cell containing mutations in the apr and npr genes, and further containing mutations in one or more of the genes encoding the Epr protease, RP-I, or RP-II, said Epr, RP-I and RP-II comprising the amino acid sequences set out in Figures 6, 10 and 14 respectively, or evolutionary homologues thereof of other Bacillus species, having protease activity, wherein said mutation results in the inhibition of the production by said cell of proteolytically active Epr protease, RP-I or RP-II.

 

 

 

 

 

 

 

 

We have a mutation in aprE and nprE and also epr and thus fall within this claim.

 

 

 

 

 

 

 

 

 

 

 

Y

 

WIDNER ET AL.

Methods for producing a polypeptide in a Bacillus cell

Patent No: US6255076B1

July 3rd, 2001

 

CLAIMS

 

COMPARISON WITH OUR METHOD

Y/N

 

1.     A method for producing a polypeptide, comprising:

2.     

(a) cultivating a Bacillus cell in a medium conducive for the production of the polypeptide, wherein the Bacillus cell comprises a nucleic acid construct comprising a tandem promoter in which each promoter sequence of the tandem promoter is operably linked to a nucleic acid sequence encoding the polypeptide, wherein the tandem promoter comprises promoters selected from the group consisting of the amyL promoter, amyQ promoter, aprH promoter, cryIIIA promoter, subtilisin Carlsberg gene promoter, and consensus promoters of the amyL promoter, amyQ promoter, aprH promoter, cryIIIA promoter, and subtilisin Carlsberg gene promoter having the sequence TTGACA for the _35” region and TATAAT for the “_10” region; and

(b) isolating the polypeptide from the cultivation medium.

 

 

 

We do not have a tandem promoter series, therefore we fall outside of this claim.

 

We are also using the … promoter, which is not listed there.

 

We will be cultivating the medium for polypeptide isolation however.

 

 

 

 

 

 

 

 

N

 

11. A method for producing a polypeptide, comprising:

(a) cultivating a Bacillus cell in a medium conducive for the production of the polypeptide, wherein the Bacillus cell comprises a nucleic acid construct comprising

(i) a consensus promoter obtained from Bacillus amyloliquefaciens alpha-amylase gene (amy Q) or Bacillus subtilis alpha-amylase gene (amy E) having the sequence TTGACA for the _35” region and TATAAT for the “_10” region operably linked to a single copy of a nucleic acid sequence encoding the polypeptide and

(ii) an mRNA processing/stabilizing sequence located downstream of the consensus promoter and upstream of the nucleic acid sequence encoding the polypeptide; and

(b) isolating the polypeptide from the cultivation medium.

 

 

 

Arguable – how to define whether the medium we will use will be ‘conductive’ or not is vague.

 

We are not using a consensus promoter from Bacillus amyloliquefaciens, but are using the Bacillus subtilis strain. The promoter we have selected is p-Spac

 

We also do not have an mRNA processing or stabilising sequence in our gblock.

We are isolating our polypeptide from the cultivation medium.

 

 

N

 

BEDZYK ET AL.

Natural promoters for gene expression and metabolic monitoring in Bacillus species

Patent No: EP1294909 A2

June 29th, 2001

 

CLAIMS

 

COMPARISON WITH OUR METHOD

Y/N

 

Legal Status: abandoned patent

Once a patent is abandoned it does not have any effect.

 

N

 

A method for the expression of a coding region of interest in a Bacillus sp comprising:

a) providing a transformed Bacillus sp cell having a chimeric gene comprising a nucleic acid fragment comprising the promoter region of a Bacillus gene operably linked to a coding region of interest expressible in a Bacillus sp, wherein the nucleic acid fragment comprising the promoter region of a Bacillus gene is selected from the group consisting of narGHJT, csnyncM, yvyD, yvaWXY, ydjL, sunA, and yolIJK and homologues thereof; and

b) growing the transformed Bacillus sp cell of step (a) in the absence of oxygen wherein the chimeric gene of step (a) is expressed.

 

 

 

Although we do use the yncM tag mentioned in this patent – however their use of YncM is as a nucleic acid fragment in the promoter region which is distinct from our purpose.

N

3. Orange Book/FDA


We also considered patents without single chain insulin to identify whether existing commercial / FDA products involved patented methods eg. storage etc., that may be broad enough to include insulin analogues like Winsulin.

Looking through the Orange Book, a drug database showing all products that have been approved - including their therapeutic equivalences, our team searched through all 101 entries that involved insulin to determine whether or not we would fall under a patent here.

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